Add metamap for input/output in stringtie/merge

modules/nf-core/stringtie/merge/main.nf

@@ -1,37 +1,41 @@
 process STRINGTIE_MERGE {
+    tag "${meta.id}"
     label 'process_medium'
 
     // Note: 2.7X indices incompatible with AWS iGenomes.
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/stringtie:2.2.1--hecb563c_2' :
-        'biocontainers/stringtie:2.2.1--hecb563c_2' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/stringtie:2.2.1--hecb563c_2'
+        : 'biocontainers/stringtie:2.2.1--hecb563c_2'}"
 
     input:
-    path stringtie_gtf
-    path annotation_gtf
+    tuple val(meta), path(gtf)
+    tuple val(meta2), path(annotation_gtf)
 
     output:
-    path "stringtie.merged.gtf", emit: gtf
+    tuple val(meta), path("${prefix}.gtf"), emit: merged_gtf
     tuple val("${task.process}"), val('stringtie'), eval('stringtie --version'), emit: versions_stringtie, topic: versions
+
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args      = task.ext.args ?: ''
-    def reference = annotation_gtf ? "-G $annotation_gtf" : ""
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    def reference = annotation_gtf ? "-G ${annotation_gtf}" : ""
     """
     stringtie \\
-        --merge $stringtie_gtf \\
-        $reference \\
-        -o stringtie.merged.gtf \\
-        $args
-
+        --merge \\
+        ${gtf} \\
+        ${reference} \\
+        -o ${prefix}.gtf \\
+        -p ${task.cpus} \\
+        ${args}
     """
 
     stub:
+    prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch stringtie.merged.gtf
-
+    touch ${prefix}.gtf
     """
 }

modules/nf-core/stringtie/merge/meta.yml

@@ -14,25 +14,32 @@ tools:
         - "MIT"
       identifier: biotools:stringtie
 input:
-  - stringtie_gtf:
-      type: file
-      description: |
-        Stringtie transcript gtf output(s).
-      pattern: "*.gtf"
-      ontologies: []
-  - annotation_gtf:
-      type: file
-      description: |
-        Annotation gtf file (optional).
-      pattern: "*.gtf"
-      ontologies: []
-output:
-  gtf:
-    - stringtie.merged.gtf:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - gtf:
         type: file
-        description: Merged gtf file
-        pattern: "stringtie.merged.gtf"
-        ontologies: []
+        description: |
+          Stringtie transcript gtf output(s) to be merged together.
+        pattern: "*.{gtf|gff}"
+        ontologies:
+          - edam: "http://edamontology.org/format_2306"
+          - edam: "http://edamontology.org/format_1975"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - annotation_gtf:
+        type: file
+        description: |
+          Reference annotation gtf file (optional).
+        pattern: "*.{gtf}"
+        ontologies:
+          - edam: "http://edamontology.org/format_2306"
+output:
   versions_stringtie:
     - - ${task.process}:
           type: string
@@ -43,6 +50,19 @@ output:
       - stringtie --version:
           type: eval
           description: The expression to obtain the version of the tool
+  merged_gtf:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}.gtf:
+          type: file
+          description: A unified non-redundant set of isoforms from the provided
+            gtf files.
+          pattern: "${prefix}.{gtf}"
+          ontologies:
+            - edam: "http://edamontology.org/format_2306"
 topics:
   versions:
     - - ${task.process}:

modules/nf-core/stringtie/merge/tests/main.nf.test

@@ -29,17 +29,18 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = STRINGTIE_STRINGTIE.out.transcript_gtf.map { it -> it[1] }
-                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true)
+                input[0] = STRINGTIE_STRINGTIE.out.transcript_gtf
+                input[1] = [[id:'ref', strandedness:'forward'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
                 """
             }
         }
 
         then {
             assertAll(
             { assert process.success },
-            { assert snapshot(process.out.gtf).match("fs_gtf") },
-            { assert snapshot(process.out.findAll { key, val -> key.startsWith('versions') }).match("fs_versions") }
+            { assert snapshot(
+                sanitizeOutput(process.out)
+                ).match() }
             )
         }
     }
@@ -49,17 +50,18 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = STRINGTIE_STRINGTIE.out.transcript_gtf.map { it -> it[1] }
-                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true)
+                input[0] = STRINGTIE_STRINGTIE.out.transcript_gtf
+                input[1] = [[id:'ref', strandedness:'reverse'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
                 """
             }
         }
 
         then {
             assertAll(
             { assert process.success },
-            { assert snapshot(process.out.gtf).match("rs_gtf") },
-            { assert snapshot(process.out.findAll { key, val -> key.startsWith('versions') }).match("rs_versions") }
+            { assert snapshot(
+                sanitizeOutput(process.out)
+                ).match() }
             )
         }
     }

modules/nf-core/stringtie/merge/tests/main.nf.test.snap

@@ -1,7 +1,16 @@
 {
-    "rs_versions": {
+    "homo_sapiens - forward strandedness": {
         "content": [
             {
+                "merged_gtf": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "reverse"
+                        },
+                        "test.gtf:md5,40780dc05eff7cf2c77705f857768441"
+                    ]
+                ],
                 "versions_stringtie": [
                     [
                         "STRINGTIE_MERGE",
@@ -11,39 +20,24 @@
                 ]
             }
         ],
-        "timestamp": "2026-04-01T10:23:50.809860959",
+        "timestamp": "2026-04-08T13:02:20.089324763",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.4"
         }
     },
-    "rs_gtf": {
-        "content": [
-            [
-                "stringtie.merged.gtf:md5,6da479298d73d5b3216d4e1576a2bdf4"
-            ]
-        ],
-        "timestamp": "2023-11-23T14:14:39.691894799",
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        }
-    },
-    "fs_gtf": {
-        "content": [
-            [
-                "stringtie.merged.gtf:md5,6da479298d73d5b3216d4e1576a2bdf4"
-            ]
-        ],
-        "timestamp": "2024-02-07T16:43:48.130184",
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        }
-    },
-    "fs_versions": {
+    "homo_sapiens - reverse strandedness": {
         "content": [
             {
+                "merged_gtf": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "reverse"
+                        },
+                        "test.gtf:md5,40780dc05eff7cf2c77705f857768441"
+                    ]
+                ],
                 "versions_stringtie": [
                     [
                         "STRINGTIE_MERGE",
@@ -53,7 +47,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-04-01T10:22:57.308138643",
+        "timestamp": "2026-04-08T13:02:52.305961798",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.4"

subworkflows/nf-core/bam_stringtie_merge/main.nf

@@ -1,33 +1,28 @@
 include { STRINGTIE_STRINGTIE } from '../../../modules/nf-core/stringtie/stringtie/main'
-include { STRINGTIE_MERGE    } from '../../../modules/nf-core/stringtie/merge/main'
+include { STRINGTIE_MERGE     } from '../../../modules/nf-core/stringtie/merge/main'
 
 
 workflow BAM_STRINGTIE_MERGE {
-
     take:
     bam_sorted // channel: [ meta, bam ]
-    ch_chrgtf  // channel: [ meta, gtf ]
+    ch_chrgtf // channel: [ meta, gtf ]
 
     main:
-    ch_versions       = channel.empty()
     ch_stringtie_gtfs = channel.empty()
 
     STRINGTIE_STRINGTIE(
         bam_sorted,
-        ch_chrgtf.map { _meta, gtf -> [ gtf ] }
+        ch_chrgtf.map { _meta, gtf -> [gtf] },
     )
 
-    STRINGTIE_STRINGTIE.out.transcript_gtf
-        .map { _meta, gtf -> [ gtf ] }
-        .set { stringtie_gtfs }
+    STRINGTIE_STRINGTIE.out.transcript_gtf.set { stringtie_gtfs }
 
     STRINGTIE_MERGE(
         stringtie_gtfs,
-        ch_chrgtf.map { _meta, gtf -> [ gtf ] }
+        ch_chrgtf
     )
-    ch_stringtie_gtfs = STRINGTIE_MERGE.out.gtf
+    ch_stringtie_gtfs = STRINGTIE_MERGE.out.merged_gtf
 
     emit:
     stringtie_gtf = ch_stringtie_gtfs // channel: [ meta, gtf ]
-    versions      = ch_versions                     // channel: [ path(versions.yml) ]
 }

subworkflows/nf-core/bam_stringtie_merge/tests/main.nf.test

@@ -30,7 +30,9 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(workflow.out).match() },
+                { assert snapshot(
+                    sanitizeOutput(workflow.out)
+                    ).match() },
             )
         }
     }

subworkflows/nf-core/bam_stringtie_merge/tests/main.nf.test.snap

@@ -2,21 +2,18 @@
     "Should run stringtie subworkflow": {
         "content": [
             {
-                "0": [
-                    "stringtie.merged.gtf:md5,6da479298d73d5b3216d4e1576a2bdf4"
-                ],
-                "1": [
-
-                ],
                 "stringtie_gtf": [
-                    "stringtie.merged.gtf:md5,6da479298d73d5b3216d4e1576a2bdf4"
-                ],
-                "versions": [
-
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "reverse"
+                        },
+                        "test.gtf:md5,40780dc05eff7cf2c77705f857768441"
+                    ]
                 ]
             }
         ],
-        "timestamp": "2026-04-01T10:24:43.783356616",
+        "timestamp": "2026-04-08T13:03:23.975567558",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.4"